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Chen KQ, Kawakami H, Anderson A, Corcoran D, Soni A, Nishinakamura R, Kawakami Y. Sall genes regulate hindlimb initiation in mouse embryos. Genetics 2024; 227:iyae029. [PMID: 38386912 PMCID: PMC11075541 DOI: 10.1093/genetics/iyae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 01/15/2024] [Accepted: 02/14/2024] [Indexed: 02/24/2024] Open
Abstract
Vertebrate limbs start to develop as paired protrusions from the lateral plate mesoderm at specific locations of the body with forelimb buds developing anteriorly and hindlimb buds posteriorly. During the initiation process, limb progenitor cells maintain active proliferation to form protrusions and start to express Fgf10, which triggers molecular processes for outgrowth and patterning. Although both processes occur in both types of limbs, forelimbs (Tbx5), and hindlimbs (Isl1) utilize distinct transcriptional systems to trigger their development. Here, we report that Sall1 and Sall4, zinc finger transcription factor genes, regulate hindlimb initiation in mouse embryos. Compared to the 100% frequency loss of hindlimb buds in TCre; Isl1 conditional knockouts, Hoxb6Cre; Isl1 conditional knockout causes a hypomorphic phenotype with only approximately 5% of mutants lacking the hindlimb. Our previous study of SALL4 ChIP-seq showed SALL4 enrichment in an Isl1 enhancer, suggesting that SALL4 acts upstream of Isl1. Removing 1 allele of Sall4 from the hypomorphic Hoxb6Cre; Isl1 mutant background caused loss of hindlimbs, but removing both alleles caused an even higher frequency of loss of hindlimbs, suggesting a genetic interaction between Sall4 and Isl1. Furthermore, TCre-mediated conditional double knockouts of Sall1 and Sall4 displayed a loss of expression of hindlimb progenitor markers (Isl1, Pitx1, Tbx4) and failed to develop hindlimbs, demonstrating functional redundancy between Sall1 and Sall4. Our data provides genetic evidence that Sall1 and Sall4 act as master regulators of hindlimb initiation.
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Affiliation(s)
- Katherine Q Chen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Hiroko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Aaron Anderson
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Dylan Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Aditi Soni
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ryuichi Nishinakamura
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA
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Long J, Mariossi A, Cao C, Mo Z, Thompson JW, Levine MS, Lemaire LA. Cereblon influences the timing of muscle differentiation in Ciona tadpoles. Proc Natl Acad Sci U S A 2023; 120:e2309989120. [PMID: 37856545 PMCID: PMC10614628 DOI: 10.1073/pnas.2309989120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/09/2023] [Indexed: 10/21/2023] Open
Abstract
Thalidomide has a dark history as a teratogen, but in recent years, its derivates have been shown to function as potent chemotherapeutic agents. These drugs bind cereblon (CRBN), the substrate receptor of an E3 ubiquitin ligase complex, and modify its degradation targets. Despite these insights, remarkably little is known about the normal function of cereblon in development. Here, we employ Ciona, a simple invertebrate chordate, to identify endogenous Crbn targets. In Ciona, Crbn is specifically expressed in developing muscles during tail elongation before they acquire contractile activity. Crbn expression is activated by Mrf, the ortholog of MYOD1, a transcription factor important for muscle differentiation. CRISPR/Cas9-mediated mutations of Crbn lead to precocious onset of muscle contractions. By contrast, overexpression of Crbn delays contractions and is associated with decreased expression of contractile protein genes such as troponin. This reduction is possibly due to reduced Mrf protein levels without altering Mrf mRNA levels. Our findings suggest that Mrf and Crbn form a negative feedback loop to control the precision of muscle differentiation during tail elongation.
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Affiliation(s)
- Juanjuan Long
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | - Andrea Mariossi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | - Chen Cao
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | | | | | - Michael S. Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
- Department of Molecular Biology, Princeton University, Princeton, NJ08544
| | - Laurence A. Lemaire
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
- Department of Biology, Saint Louis University, St. Louis, MO63103
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Kawakami H, Chen KQ, Zhang R, Pappas MP, Bailey A, Reisz JA, Corcoran D, Nishinakamura R, D'Alessandro A, Kawakami Y. Sall4 restricts glycolytic metabolism in limb buds through transcriptional regulation of glycolytic enzyme genes. Dev Biol 2023; 501:28-38. [PMID: 37301463 PMCID: PMC10330914 DOI: 10.1016/j.ydbio.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/09/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
Recent studies illustrate the importance of regulation of cellular metabolism, especially glycolysis and pathways branching from glycolysis, during vertebrate embryo development. For example, glycolysis generates cellular energy ATP. Glucose carbons are also directed to the pentose phosphate pathway, which is needed to sustain anabolic processes in the rapidly growing embryos. However, our understanding of the exact status of glycolytic metabolism as well as genes that regulate glycolytic metabolism are still incomplete. Sall4 is a zinc finger transcription factor that is highly expressed in undifferentiated cells in developing mouse embryos, such as blastocysts and the post-implantation epiblast. TCre; Sall4 conditional knockout mouse embryos exhibit various defects in the posterior part of the body, including hindlimbs. Using transcriptomics approaches, we found that many genes encoding glycolytic enzymes are upregulated in the posterior trunk, including the hindlimb-forming region, of Sall4 conditional knockout mouse embryos. In situ hybridization and qRT-PCR also confirmed upregulation of expression of several glycolytic genes in hindlimb buds. A fraction of those genes are bound by SALL4 at the promoters, gene bodies or distantly-located regions, suggesting that Sall4 directly regulates expression of several glycolytic enzyme genes in hindlimb buds. To further gain insight into the metabolic status associated with the observed changes at the transcriptional level, we performed a comprehensive analysis of metabolite levels in limb buds in wild type and Sall4 conditional knockout embryos by high-resolution mass spectrometry. We found that the levels of metabolic intermediates of glycolysis are lower, but glycolytic end-products pyruvate and lactate did not exhibit differences in Sall4 conditional knockout hindlimb buds. The increased expression of glycolytic genes would have caused accelerated glycolytic flow, resulting in low levels of intermediates. This condition may have prevented intermediates from being re-directed to other pathways, such as the pentose phosphate pathway. Indeed, the change in glycolytic metabolite levels is associated with reduced levels of ATP and metabolites of the pentose phosphate pathway. To further test whether glycolysis regulates limb patterning downstream of Sall4, we conditionally inactivated Hk2, which encodes a rate-limiting enzyme gene in glycolysis and is regulated by Sall4. The TCre; Hk2 conditional knockout hindlimb exhibited a short femur, and a lack of tibia and anterior digits in hindlimbs, which are defects similarly found in the TCre; Sall4 conditional knockout. The similarity of skeletal defects in Sall4 mutants and Hk2 mutants suggests that regulation of glycolysis plays a role in hindlimb patterning. These data suggest that Sall4 restricts glycolysis in limb buds and contributes to patterning and regulation of glucose carbon flow during development of limb buds.
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Affiliation(s)
- Hiroko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN, USA
| | - Katherine Q Chen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ruizhi Zhang
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Matthew P Pappas
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Abigail Bailey
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Dylan Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ryuichi Nishinakamura
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN, USA.
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Normal embryonic development and neonatal digit regeneration in mice overexpressing a stem cell factor, Sall4. PLoS One 2022; 17:e0267273. [PMID: 35482646 PMCID: PMC9049339 DOI: 10.1371/journal.pone.0267273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/05/2022] [Indexed: 01/29/2023] Open
Abstract
Sall4 encodes a transcription factor and is known to participate in the pluripotency network of embryonic stem cells. Sall4 expression is known to be high in early stage post-implantation mouse embryos. During early post-gastrulation stages, Sall4 is highly expressed in the tail bud and distal limb buds, where progenitor cells are maintained in an undifferentiated status. The expression of Sall4 is rapidly downregulated during embryonic development. We previously demonstrated that Sall4 is required for limb and posterior axial skeleton development by conditional deletion of Sall4 in the T (Brachyury) lineage. To gain insight into Sall4 functions in embryonic development and postnatal digit regeneration, we genetically overexpressed Sall4 in the mesodermal lineage by the TCre transgene and a novel knockin allele of Rosa26-loxP-stop-loxP-Sall4. In significant contrast to severe defects by Sall4 loss of function reported in previous studies, overexpression of Sall4 resulted in normal morphology and pattern in embryos and neonates. The length of limb long bones showed subtle reduction in Sall4-overexpression mice. It is known that the digit tip of neonatal mice has level-specific regenerative ability after experimental amputation. We observed Sall4 expression in the digit tip by using a sensitive Sall4-LacZ knock-in reporter expression. Sall4 overexpression did not alter the regenerative ability of the terminal phalange that normally regenerates after amputation. Moreover, Sall4 overexpression did not confer regenerative ability to the second phalange that normally does not regenerate after amputation. These genetic experiments show that overexpression of Sall4 does not alter the development of the appendicular and axial skeleton, or neonatal digit regeneration. The results suggest that Sall4 acts as a permissive factor rather than playing an instructive role.
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SALL Proteins; Common and Antagonistic Roles in Cancer. Cancers (Basel) 2021; 13:cancers13246292. [PMID: 34944911 PMCID: PMC8699250 DOI: 10.3390/cancers13246292] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 01/02/2023] Open
Abstract
Simple Summary Transcription factors play essential roles in regulating gene expression, impacting the cell phenotype and function, and in the response of cells to environmental conditions. Alterations in transcription factors, including gene amplification or deletion, point mutations, and expression changes, are implicated in carcinogenesis, cancer progression, metastases, and resistance to cancer treatments. Not surprisingly, transcription factor activity is altered in numerous cancers, representing a unique class of cancer drug targets. This review updates and integrates information on the SALL family of transcription factors, highlighting the synergistic and/or antagonistic functions they perform in various cancer types. Abstract SALL proteins are a family of four conserved C2H2 zinc finger transcription factors that play critical roles in organogenesis during embryonic development. They regulate cell proliferation, survival, migration, and stemness; consequently, they are involved in various human genetic disorders and cancer. SALL4 is a well-recognized oncogene; however, SALL1–3 play dual roles depending on the cancer context and stage of the disease. Current reviews of SALLs have focused only on SALL2 or SALL4, lacking an integrated view of the SALL family members in cancer. Here, we update the recent advances of the SALL members in tumor development, cancer progression, and therapy, highlighting the synergistic and/or antagonistic functions they perform in similar cancer contexts. We identified common regulatory mechanisms, targets, and signaling pathways in breast, brain, liver, colon, blood, and HPV-related cancers. In addition, we discuss the potential of the SALL family members as cancer biomarkers and in the cancer cells’ response to therapies. Understanding SALL proteins’ function and relationship will open new cancer biology, clinical research, and therapy perspectives.
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Duboc V, Sulaiman FA, Feneck E, Kucharska A, Bell D, Holder-Espinasse M, Logan MPO. Tbx4 function during hindlimb development reveals a mechanism that explains the origins of proximal limb defects. Development 2021; 148:271903. [PMID: 34423345 PMCID: PMC8497778 DOI: 10.1242/dev.199580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/02/2021] [Indexed: 11/20/2022]
Abstract
We dissect genetically a gene regulatory network that involves the transcription factors Tbx4, Pitx1 and Isl1 acting cooperatively to establish the hindlimb bud, and identify key differences in the pathways that initiate formation of the hindlimb and forelimb. Using live image analysis of murine limb mesenchyme cells undergoing chondrogenesis in micromass culture, we distinguish a series of changes in cellular behaviours and cohesiveness that are required for chondrogenic precursors to undergo differentiation. Furthermore, we provide evidence that the proximal hindlimb defects observed in Tbx4 mutant mice result from a failure in the early differentiation step of chondroprogenitors into chondrocytes, providing an explanation for the origins of proximally biased limb defects.
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Affiliation(s)
- Veronique Duboc
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Fatima A Sulaiman
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Eleanor Feneck
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Anna Kucharska
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Donald Bell
- Light Microscopy, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Malcolm P O Logan
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, UK
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Yamanaka S, Murai H, Saito D, Abe G, Tokunaga E, Iwasaki T, Takahashi H, Takeda H, Suzuki T, Shibata N, Tamura K, Sawasaki T. Thalidomide and its metabolite 5-hydroxythalidomide induce teratogenicity via the cereblon neosubstrate PLZF. EMBO J 2021; 40:e105375. [PMID: 33470442 PMCID: PMC7883055 DOI: 10.15252/embj.2020105375] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 11/17/2020] [Accepted: 11/30/2020] [Indexed: 12/17/2022] Open
Abstract
Thalidomide causes teratogenic effects by inducing protein degradation via cereblon (CRBN)‐containing ubiquitin ligase and modification of its substrate specificity. Human P450 cytochromes convert thalidomide into two monohydroxylated metabolites that are considered to contribute to thalidomide effects, through mechanisms that remain unclear. Here, we report that promyelocytic leukaemia zinc finger (PLZF)/ZBTB16 is a CRBN target protein whose degradation is involved in thalidomide‐ and 5‐hydroxythalidomide‐induced teratogenicity. Using a human transcription factor protein array produced in a wheat cell‐free protein synthesis system, PLZF was identified as a thalidomide‐dependent CRBN substrate. PLZF is degraded by the ubiquitin ligase CRL4CRBN in complex with thalidomide, its derivatives or 5‐hydroxythalidomide in a manner dependent on the conserved first and third zinc finger domains of PLZF. Surprisingly, thalidomide and 5‐hydroxythalidomide confer distinctly different substrate specificities to mouse and chicken CRBN, and both compounds cause teratogenic phenotypes in chicken embryos. Consistently, knockdown of Plzf induces short bone formation in chicken limbs. Most importantly, degradation of PLZF protein, but not of the known thalidomide‐dependent CRBN substrate SALL4, was induced by thalidomide or 5‐hydroxythalidomide treatment in chicken embryos. Furthermore, PLZF overexpression partially rescued the thalidomide‐induced phenotypes. Our findings implicate PLZF as an important thalidomide‐induced CRBN neosubstrate involved in thalidomide teratogenicity.
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Affiliation(s)
- Satoshi Yamanaka
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Hidetaka Murai
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Daisuke Saito
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Gembu Abe
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Etsuko Tokunaga
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya, Japan
| | - Takahiro Iwasaki
- Division of Proteo-Drug-Discovery Sciences, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Hirotaka Takahashi
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Hiroyuki Takeda
- Division of Proteo-Drug-Discovery Sciences, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Takayuki Suzuki
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Norio Shibata
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya, Japan
| | - Koji Tamura
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Tatsuya Sawasaki
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, Japan
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